Reorganized genomic taxonomy of francisellaceae enables design of robust environmental PCR assays for detection of francisella tularensis

Caroline Öhrman; Jason W. Sahl; Andreas Sjödin; Ingrid Uneklint; Rebecca Ballard; Linda Karlsson; Ryelan F. McDonough; David Sundell; Kathleen Soria; Stina Bäckman; Kitty Chase; Björn Brindefalk; Shanmuga Sozhamannan; Adriana Vallesi; Emil Hägglund; Jose Gustavo Ramirez-Paredes; Johanna Thelaus; Duncan Colquhoun; Kerstin Myrtennäs; Dawn Birdsell; Anders Johansson; David M. Wagner; Mats Forsman

doi:10.3390/microorganisms9010146

Reorganized genomic taxonomy of francisellaceae enables design of robust environmental PCR assays for detection of francisella tularensis

Caroline Öhrman, Jason W. Sahl, Andreas Sjödin, Ingrid Uneklint, Rebecca Ballard, Linda Karlsson, Ryelan F. McDonough, David Sundell, Kathleen Soria, Stina Bäckman, Kitty Chase, Björn Brindefalk, Shanmuga Sozhamannan, Adriana Vallesi, Emil Hägglund, Jose Gustavo Ramirez-Paredes, Johanna Thelaus, Duncan Colquhoun, Kerstin Myrtennäs, Dawn BirdsellAnders Johansson, David M. Wagner, Mats Forsman

Biological Sciences

Research output: Contribution to journal › Article › peer-review

25 Scopus citations

Abstract

In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.

Original language	English (US)
Article number	146
Pages (from-to)	1-21
Number of pages	21
Journal	Microorganisms
Volume	9
Issue number	1
DOIs	https://doi.org/10.3390/microorganisms9010146
State	Published - Jan 2021

Keywords

Assay
Francisella taxonomy
Phylogeny
Tularemia

ASJC Scopus subject areas

Microbiology
Microbiology (medical)
Virology

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10.3390/microorganisms9010146

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Öhrman, C., Sahl, J. W., Sjödin, A., Uneklint, I., Ballard, R., Karlsson, L., McDonough, R. F., Sundell, D., Soria, K., Bäckman, S., Chase, K., Brindefalk, B., Sozhamannan, S., Vallesi, A., Hägglund, E., Ramirez-Paredes, J. G., Thelaus, J., Colquhoun, D., Myrtennäs, K., ... Forsman, M. (2021). Reorganized genomic taxonomy of francisellaceae enables design of robust environmental PCR assays for detection of francisella tularensis. Microorganisms, 9(1), 1-21. Article 146. https://doi.org/10.3390/microorganisms9010146

Öhrman, C, Sahl, JW, Sjödin, A, Uneklint, I, Ballard, R, Karlsson, L, McDonough, RF, Sundell, D, Soria, K, Bäckman, S, Chase, K, Brindefalk, B, Sozhamannan, S, Vallesi, A, Hägglund, E, Ramirez-Paredes, JG, Thelaus, J, Colquhoun, D, Myrtennäs, K, Birdsell, D, Johansson, A, Wagner, DM & Forsman, M 2021, 'Reorganized genomic taxonomy of francisellaceae enables design of robust environmental PCR assays for detection of francisella tularensis', Microorganisms, vol. 9, no. 1, 146, pp. 1-21. https://doi.org/10.3390/microorganisms9010146

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abstract = "In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.",

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AU - Ballard, Rebecca

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AU - Sundell, David

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AU - Chase, Kitty

AU - Brindefalk, Björn

AU - Sozhamannan, Shanmuga

AU - Vallesi, Adriana

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AU - Ramirez-Paredes, Jose Gustavo

AU - Thelaus, Johanna

AU - Colquhoun, Duncan

AU - Myrtennäs, Kerstin

AU - Birdsell, Dawn

AU - Johansson, Anders

AU - Wagner, David M.

AU - Forsman, Mats

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N2 - In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.

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Reorganized genomic taxonomy of francisellaceae enables design of robust environmental PCR assays for detection of francisella tularensis

Abstract

Keywords

ASJC Scopus subject areas

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